Variant report

Variant	rs9924958
Chromosome Location	chr16:77246110-77246111
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:77246016-77248008	A549	lung:	n/a	n/a
2	POLR2A	chr16:77245941-77247081	HEK293	kidney:	n/a	n/a
3	SIN3AK20	chr16:77245966-77246566	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr16:77245882-77246578	GM12892	blood:	n/a	n/a
5	TAF1	chr16:77245911-77247928	A549	lung:	n/a	n/a
6	POLR2A	chr16:77246071-77246589	Raji	blood:	n/a	n/a
7	ZEB1	chr16:77245953-77246186	GM12878	blood:	n/a	n/a
8	JUND	chr16:77245976-77246284	H1-hESC	embryonic stem cell:	n/a	n/a
9	RFX5	chr16:77246038-77246200	GM12878	blood:	n/a	n/a
10	POLR2A	chr16:77245910-77246546	GM12878	blood:	n/a	n/a
11	EBF1	chr16:77246078-77246455	GM12878	blood:	n/a	n/a
12	KAP1	chr16:77245907-77246273	U2OS	brain:	n/a	n/a
13	TAF1	chr16:77246032-77246435	PFSK-1	brain:	n/a	n/a
14	EGR1	chr16:77245956-77246481	K562	blood:	n/a	chr16:77246281-77246294 chr16:77246114-77246124 chr16:77246163-77246173
15	POLR2A	chr16:77245886-77246536	SK-N-SH	brain:	n/a	n/a
16	ZBTB7A	chr16:77245881-77246937	ECC-1	luminal epithelium:	n/a	n/a
17	HA-E2F1	chr16:77245792-77246461	MCF-7	breast:	n/a	chr16:77246335-77246344
18	MAX	chr16:77245904-77247126	SK-N-SH	brain:	n/a	chr16:77246597-77246607 chr16:77246115-77246125
19	NRF1	chr16:77246082-77246267	GM12878	blood:	n/a	chr16:77246115-77246124
20	STAT1	chr16:77246039-77246301	GM12878	blood:	n/a	chr16:77246274-77246286 chr16:77246273-77246285 chr16:77246269-77246281
21	CTCF	chr16:77246080-77246230	GM12866	blood:	n/a	n/a
22	EGR1	chr16:77245690-77247060	HCT-116	colon:	n/a	chr16:77246281-77246294 chr16:77246562-77246572 chr16:77246114-77246124 chr16:77246163-77246173
23	POLR2A	chr16:77246029-77246473	MCF-7	breast:	n/a	n/a
24	REST	chr16:77245809-77246517	PFSK-1	brain:	n/a	n/a
25	CTCF	chr16:77246080-77246230	NHEK	skin:	n/a	n/a
26	TCF3	chr16:77246017-77246296	GM12878	blood:	n/a	chr16:77246105-77246118
27	HEY1	chr16:77246053-77246372	K562	blood:	n/a	chr16:77246140-77246155 chr16:77246332-77246347
28	TCF12	chr16:77245897-77246382	H1-hESC	embryonic stem cell:	n/a	n/a
29	EGR1	chr16:77246013-77246404	GM12878	blood:	n/a	chr16:77246281-77246294 chr16:77246114-77246124 chr16:77246163-77246173
30	PML	chr16:77245941-77246617	GM12878	blood:	n/a	n/a
31	EP300	chr16:77245892-77246332	H1-hESC	embryonic stem cell:	n/a	n/a
32	UBTF	chr16:77245963-77247079	K562	blood:	n/a	n/a
33	EBF1	chr16:77245990-77246389	GM12878	blood:	n/a	n/a
34	MAZ	chr16:77245924-77247050	GM12878	blood:	n/a	chr16:77246597-77246607 chr16:77246115-77246125
35	POLR2A	chr16:77246091-77246262	HepG2	liver:	n/a	n/a
36	YY1	chr16:77245859-77246569	A549	lung:	n/a	chr16:77246147-77246158 chr16:77246302-77246313 chr16:77246309-77246318
37	YY1	chr16:77246001-77246520	GM12892	blood:	n/a	chr16:77246147-77246158 chr16:77246302-77246313 chr16:77246309-77246318
38	BHLHE40	chr16:77246069-77246442	GM12878	blood:	n/a	n/a
39	RCOR1	chr16:77245971-77247052	K562	blood:	n/a	n/a
40	EGR1	chr16:77245975-77246554	H1-hESC	embryonic stem cell:	n/a	chr16:77246281-77246294 chr16:77246114-77246124 chr16:77246163-77246173
41	SP1	chr16:77245631-77248366	HCT-116	colon:	n/a	chr16:77246115-77246125 chr16:77245959-77245971 chr16:77247070-77247079 chr16:77246122-77246131 chr16:77246336-77246348 chr16:77245964-77245976 chr16:77246118-77246132 chr16:77246114-77246126 chr16:77246115-77246124 chr16:77246338-77246347 chr16:77246561-77246573 chr16:77245966-77245975 chr16:77246982-77246994 chr16:77246203-77246214 chr16:77245959-77245971 chr16:77246596-77246608 chr16:77245964-77245976 chr16:77246558-77246572 chr16:77246562-77246571 chr16:77246982-77246994 chr16:77247069-77247078 chr16:77246336-77246348 chr16:77245961-77245970 chr16:77246337-77246346 chr16:77246983-77246993 chr16:77246561-77246573 chr16:77245960-77245969 chr16:77246114-77246126 chr16:77246563-77246572 chr16:77246116-77246125 chr16:77246738-77246747 chr16:77246291-77246305
42	POLR2A	chr16:77245904-77246540	U87	brain:	n/a	n/a
43	YY1	chr16:77246009-77246563	ECC-1	luminal epithelium:	n/a	chr16:77246147-77246158 chr16:77246302-77246313 chr16:77246309-77246318
44	YY1	chr16:77246080-77246391	K562	blood:	n/a	chr16:77246147-77246158 chr16:77246302-77246313 chr16:77246309-77246318
45	FOXP2	chr16:77245924-77246378	PFSK-1	brain:	n/a	n/a
46	GATA3	chr16:77245742-77248440	A549	lung:	n/a	chr16:77247924-77247933 chr16:77248147-77248155 chr16:77248276-77248283
47	SP1	chr16:77245821-77246875	A549	lung:	n/a	chr16:77246115-77246125 chr16:77245959-77245971 chr16:77246122-77246131 chr16:77246336-77246348 chr16:77245964-77245976 chr16:77246118-77246132 chr16:77246114-77246126 chr16:77246115-77246124 chr16:77246338-77246347 chr16:77246561-77246573 chr16:77245966-77245975 chr16:77246203-77246214 chr16:77245959-77245971 chr16:77246596-77246608 chr16:77245964-77245976 chr16:77246558-77246572 chr16:77246562-77246571 chr16:77246336-77246348 chr16:77245961-77245970 chr16:77246337-77246346 chr16:77246561-77246573 chr16:77245960-77245969 chr16:77246114-77246126 chr16:77246563-77246572 chr16:77246116-77246125 chr16:77246738-77246747 chr16:77246291-77246305
48	YY1	chr16:77245948-77246575	HepG2	liver:	n/a	chr16:77246147-77246158 chr16:77246302-77246313 chr16:77246309-77246318
49	MAX	chr16:77245808-77247080	ECC-1	luminal epithelium:	n/a	chr16:77246597-77246607 chr16:77246115-77246125
50	POLR2A	chr16:77245922-77246941	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:77224814..77227187-chr16:77245098..77247161,3	K562	blood:
2	chr16:77223598..77226407-chr16:77245076..77246907,2	MCF-7	breast:
3	chr16:77223923..77226639-chr16:77244818..77248823,8	K562	blood:
4	chr16:77225300..77227094-chr16:77244120..77246217,2	MCF-7	breast:

Variant related genes	Relation type
SYCE1L	TF binding region
ENSG00000103111	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1019565	1.00[ASN][1000 genomes]
rs11149971	1.00[ASN][1000 genomes]
rs11544783	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860898	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11863718	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12931673	0.90[ASN][1000 genomes]
rs13329731	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13329816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13330279	1.00[ASN][1000 genomes]
rs13330367	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13332812	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13336198	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337994	0.90[ASN][1000 genomes]
rs13339324	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1428838	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1428839	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2017197	1.00[ASN][1000 genomes]
rs28539358	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61746433	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564417	0.90[ASN][1000 genomes]
rs7184776	0.91[ASN][1000 genomes]
rs7188241	0.90[ASN][1000 genomes]
rs719053	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7198006	0.90[ASN][1000 genomes]
rs7198588	0.90[ASN][1000 genomes]
rs7201284	0.91[ASN][1000 genomes]
rs7203467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73627401	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73633620	0.90[ASN][1000 genomes]
rs73633624	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73633633	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73633644	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73633647	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73633654	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73633661	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7501191	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8048478	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925431	0.89[AMR][1000 genomes]
rs9929722	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9931082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9931400	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9935921	0.90[ASN][1000 genomes]
rs9936182	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9937408	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9937693	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9938871	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065343	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv542965	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77227200-77247200	Weak transcription	Hela-S3	cervix
2	chr16:77245400-77247200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr16:77245600-77246200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr16:77245600-77246200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr16:77245600-77246200	Flanking Active TSS	Pancreas	Pancrea
6	chr16:77245600-77246200	Flanking Active TSS	HUVEC	blood vessel
7	chr16:77245600-77246400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr16:77245600-77246400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr16:77245600-77246400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr16:77245600-77246800	Flanking Bivalent TSS/Enh	HepG2	liver
11	chr16:77245600-77247200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr16:77245600-77247200	Active TSS	Brain Germinal Matrix	brain
13	chr16:77245600-77247400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr16:77245600-77247400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:77245800-77246200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr16:77245800-77246200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
17	chr16:77245800-77246200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
18	chr16:77245800-77246200	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr16:77245800-77246200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr16:77245800-77246200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr16:77245800-77246200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr16:77245800-77246200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr16:77245800-77246200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr16:77245800-77246200	Active TSS	Colon Smooth Muscle	Colon
25	chr16:77245800-77246200	Flanking Active TSS	Esophagus	oesophagus
26	chr16:77245800-77246200	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr16:77245800-77246200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr16:77245800-77246200	Flanking Active TSS	GM12878-XiMat	blood
29	chr16:77245800-77246400	Flanking Active TSS	HMEC	breast
30	chr16:77245800-77246600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:77245800-77246600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr16:77245800-77246600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr16:77245800-77246600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr16:77245800-77246600	Active TSS	Colonic Mucosa	Colon
35	chr16:77245800-77246600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
36	chr16:77245800-77246800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr16:77245800-77247000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr16:77245800-77247000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr16:77245800-77247000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr16:77245800-77247000	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr16:77245800-77247000	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr16:77245800-77247000	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr16:77245800-77247000	Bivalent/Poised TSS	Fetal Stomach	stomach
44	chr16:77245800-77247200	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr16:77245800-77247200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr16:77245800-77247200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr16:77245800-77247200	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr16:77245800-77247200	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr16:77245800-77247200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr16:77245800-77247200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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